Yes, don't worry. Most of the processes will work with film images just fine. You may have some troubles with those processes aimed for linear data, such as all the deconvolutions. Anyway, with the use of masks, and forgiving the "theorical background", it may still be of good benefit for your images. Also you may find trouble with GREYCStoration, since it was created for digital camera's noise reduction, but you still have ACDNR and wavelets to do that job (and SCNR). So, to sumarize, just go ahead
Oh, btw, I believe that with the current image processing tools you'll be able to get better results than in the past. If it were not for the digital cameras, results from film would be getting better and better each day. Most of the techniques apply just the same.
I think that your project is worth a try. Combining the Ha data to the RGB ccd would not be an easy task, although. I would process both sets up to a certain point where they look pleasant to the eye, and then perform the combination. The luminance match will be the hardest part. You may try the color correction procedure I'm using with the HDRC process. I've tried that to fix saturation artegacts generated by deconvolutions, and it worked like a charm. I'm planning to write a standalone process with this procedure this week. With it, your combination should be easier.
Other than that, I may be a little concern about the different sampling size, and also by the different amount (and size) of the stars. That would be tricky too.
Anyway, it is a very nice experiment
and would generate results very special. If you are capable of generate a new, fresh look of our well known objects, even when it is not sharper, deeper, etc etc., then it will be worh all the effort. I'd love to see what happens. Keep us informed!
PS: Stacking film images does improve SNR a great deal. I used to combine up to a dozen exposures, and it was amazing how smooth it got, and how much details I was able to get.